A sample processing system comprising: a transporting apparatus for transporting samples to a first loading position, a second loading position, and a third loading position; a first sample processing apparatus capable of being set in a first setting position and a third setting position; a second sample processing apparatus capable of being set in a second setting position; and a controller including a memory under control of a processor, the memory storing instructions enabling the processor to carry out operations comprising: controlling the transporting apparatus so as to transport a sample to the first loading position when the first sample processing apparatus is set in the first setting position; and controlling the transporting apparatus so as to transport a sample to the third loading position when the first sample processing apparatus is set in the third setting position, is disclosed. A sample processing method and a computer program product are also disclosed.